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- PDB-6ckt: Crystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate... -

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Basic information

Entry
Database: PDB / ID: 6ckt
TitleCrystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase from Legionella pneumophila Philadelphia 1
Components2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
KeywordsTRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytoplasm
Similarity search - Function
Tetrahydrodipicolinate N-succinyltransferase, transferase hexapeptide repeat family / Tetrahydrodipicolinate-N-succinyltransferase, chain A, domain 1 / Tetrahydrodipicolinate-N-succinyltransferase, N-terminal domain superfamily / Tetrahydrodipicolinate N-succinyltransferase N-terminal / Hexapeptide repeat of succinyl-transferase / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase from Legionella pneumophila Philadelphia 1
Authors: Abendroth, J. / Allaire, M. / Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionFeb 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3254
Polymers31,1381
Non-polymers1863
Water2,414134
1
A: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
hetero molecules

A: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
hetero molecules

A: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,97412
Polymers93,4153
Non-polymers5599
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11830 Å2
ΔGint-40 kcal/mol
Surface area30150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.730, 101.730, 70.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

21A-502-

HOH

31A-529-

HOH

41A-534-

HOH

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Components

#1: Protein 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase / Tetrahydrodipicolinate N-succinyltransferase / Tetrahydropicolinate succinylase


Mass: 31138.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: dapD, lpg0888 / Plasmid: LepnA.00002.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3)
References: UniProt: Q5ZX45, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Optimization screen based on RigakuReagents JCSG+ screen B4 and Microlytic MCSG1 screen B4: 11% PEG 8000, 100Mm HEPES free acid/NaOH pH 7.0: LepnA.00002.a.B1.PS38381 at 20mg/ml: cryo: 25% EG: ...Details: Optimization screen based on RigakuReagents JCSG+ screen B4 and Microlytic MCSG1 screen B4: 11% PEG 8000, 100Mm HEPES free acid/NaOH pH 7.0: LepnA.00002.a.B1.PS38381 at 20mg/ml: cryo: 25% EG: tray 298088d1: puck FVT5-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2018
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.8→37.428 Å / Num. obs: 25336 / % possible obs: 99.8 % / Redundancy: 5.028 % / Biso Wilson estimate: 35.31 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.031 / Rrim(I) all: 0.035 / Χ2: 1.056 / Net I/σ(I): 20.77
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.855.1260.453.0318810.9370.50299.7
1.85-1.94.9260.3343.8918120.9680.374100
1.9-1.955.0820.2535.3717830.9790.28299.8
1.95-2.015.1490.1837.3317090.9880.204100
2.01-2.084.9810.1419.4417010.9920.15899.9
2.08-2.155.2920.10211.9616290.9970.11399.9
2.15-2.235.2070.08614.4915370.9970.09699.9
2.23-2.325.0770.07217.4915220.9970.0899.8
2.32-2.434.8170.05720.0714680.9980.06499.9
2.43-2.555.0930.05122.5413500.9990.05799.8
2.55-2.684.7630.04725.7213140.9980.05399.7
2.68-2.855.0740.0430.7212420.9990.04599.8
2.85-3.044.9970.03536.4411480.9990.03999.7
3.04-3.294.7750.03439.2710870.9990.03899.3
3.29-3.64.6810.03142.089850.9990.03599.4
3.6-4.034.8370.02845.128970.9990.03199.2
4.03-4.655.2440.02547.928030.9990.02799.8
4.65-5.695.2270.02348.1766910.02699.4
5.69-8.054.9810.02146.8451510.02399.4
8.05-37.4285.2390.01848.852840.9990.0298.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3026)refinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3tk8 as per Morda

3tk8


Resolution: 1.8→37.428 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 25.48
RfactorNum. reflection% reflection
Rfree0.1879 1946 7.69 %
Rwork0.1574 --
obs0.1599 25307 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.12 Å2 / Biso mean: 52.3286 Å2 / Biso min: 19.25 Å2
Refinement stepCycle: final / Resolution: 1.8→37.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 12 134 2172
Biso mean--54.41 50.71 -
Num. residues----273
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8001-1.84510.30241500.255916681818100
1.8451-1.8950.29161280.228316871815100
1.895-1.95070.26471220.196616491771100
1.9507-2.01370.20471340.180216821816100
2.0137-2.08570.21621500.166916771827100
2.0857-2.16920.21021110.16417061817100
2.1692-2.26790.22841340.171916831817100
2.2679-2.38740.23811350.159516551790100
2.3874-2.5370.19981480.172917001848100
2.537-2.73280.21261500.189416211771100
2.7328-3.00770.22771340.175616861820100
3.0077-3.44260.17361580.16541633179199
3.4426-4.33630.1761470.13916501797100
4.3363-37.43650.15031450.1341664180999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.53394.839-2.68734.4907-2.07531.661-0.3954-0.3539-0.9277-0.91140.2911-1.30510.03370.85090.07460.76610.2411-0.06381.0638-0.24111.05975.0432-23.0134-36.462
25.8978-0.1617-1.33390.1730.68125.0713-0.2346-0.9258-0.27160.3968-0.20770.74280.6162-0.74690.24730.3937-0.23730.13481.1383-0.10990.8266-32.4572-16.2782-11.7062
36.7007-1.06472.37090.2879-0.20831.07910.0104-1.27510.42520.5965-0.1940.7449-0.1008-1.14990.270.4534-0.02790.1320.8484-0.09010.8135-27.6436-8.3003-6.8565
42.93690.27840.5132.29980.41211.93270.09-0.0601-0.51130.1222-0.07110.30840.3487-0.3138-0.02380.2539-0.05360.00420.23970.00950.3205-10.7888-11.6007-12.3287
51.79240.206-0.41231.6915-0.79333.60770.07980.7137-0.4307-0.66520.03220.24620.2068-0.0988-0.10110.4875-0.0139-0.07910.5004-0.16220.3225-7.3632-11.0712-35.5216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 256 through 271 )A256 - 271
2X-RAY DIFFRACTION2chain 'A' and (resid -1 through 13 )A-1 - 13
3X-RAY DIFFRACTION3chain 'A' and (resid 14 through 39 )A14 - 39
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 151 )A40 - 151
5X-RAY DIFFRACTION5chain 'A' and (resid 152 through 255 )A152 - 255

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